Matt Snyder
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Hi Genevieve Brandt (she/her), Sorry, I know this issue is ancient. I did use `--LENIENT_HEADER true` and just re-tried with Version:2.27.4-SNAPSHOT and got the same result. MAPPINGS_DIFFER, UNMAPP...
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Thanks, Genevieve Brandt (she/her)! I will try merging the bam files first. This also makes sense because then I only have to sort one BAM file instead of dozens. Do you have a recommended number ...
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Hi again Pamela, I noticed that this helpful article points out that VQSR works best on cohort VCFs with at least 30 samples. In our organization we do not create cohort VCFs. Each VCF is only for ...
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Hi Pamela, In the end it only works if I up the --max-attempts and drop the --max-gaussians. But it works! I am also running with "-mode BOTH", but the article you linked says "Note that VQSR must ...
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This is super useful. However, none of the WDL workflows linked at the top actually use VariantRecalibrator or ApplyVQSR. It would be nice if there was an example workflow somewhere using these too...
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I just ran HaplotypeCaller and got the error below. Clearly my input is not properly named. That is easily fixable and is not an issue. A USER ERROR has occurred: Couldn't read file /home/dnanexus...